ArticleThe Journal of cell biology2024
Unbiased MD simulations identify lipid binding sites in lipid transfer proteins.
Article in The Journal of cell biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Article
- The LiPP Benchmark Set for Modeling Lipid-Protein Complexes: Comparison of Co-Folding and Docking Methods.Journal of chemical information and modeling · 2026Article
- Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation.The EMBO journal · 2026Article
- Emerging roles of lipids in the flavivirus life cycle.Trends in microbiology · 2026Review
- Mechanistic dissection of BLTP2 targeting to ER-PM contact sites.bioRxiv : the preprint server for biology · 2026Article
- A bridge-like lipid transfer protein is critical for generation of invasive stages in malaria parasites.Nature communications · 2026Article
- Article
- The molecular mechanism of lipid uptake by membrane-anchored bridge-like lipid transfer proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Identifying and Characterizing Lipid-Binding Cavities in Lipid Transfer Proteins With CG-MD Simulations.Bio-protocol · 2025Article
- ATG2A-mediated DAG transfer recruits DGAT2 for lipid droplet growth.Nature structural & molecular biology · 2025Article
- How doesScience advances · 2025Article
- Impaired hematopoiesis and embryonic lethality at midgestation of mice lacking both lipid transfer proteins VPS13A and VPS13C.PLoS biology · 2025Article
- Pex30-dependent membrane contact sites maintain ER lipid homeostasis.The Journal of cell biology · 2025Article
- Article
- VPS13 and bridge-like lipid transporters, mechanisms, and mysteries.Frontiers in neuroscience · 2025Review
- Making lipids very unhappy to discover how they bind to proteins.The Journal of cell biology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.
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Registered trials
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